Merge branch 'integrate_h5tonx' into 'master'

Integrate dicttinexus

See merge request workflow/est!39

est/io/io.py

@@ -31,7 +31,7 @@ import logging
 from datetime import datetime
 import h5py
 import numpy
-from silx.io.dictdump import dicttoh5, h5todict
+from silx.io.dictdump import dicttoh5, h5todict, dicttonx
 from silx.io.url import DataUrl
 from silx.utils.enum import Enum
 from est.units import ur
@@ -42,6 +42,7 @@ from est.io.utils import get_data
 import silx.io.h5py_utils
 from silx.io.h5py_utils import File as HDF5File
 from est import settings
+import json
 
 try:
     from est.io.utils.larch import read_ascii as larch_read_ascii
@@ -444,8 +445,6 @@ def write_xas_proc(
 
         with HDF5File(h5_file, "a") as h5f:
             plot_group = h5f.require_group(plot_path)
-            plot_group.attrs["NX_class"] = "NXdata"
-            plot_group.attrs["interpretation"] = "spectrum"
             assert plot.signal is not None
             assert plot.axes is not None
 
@@ -478,7 +477,6 @@ def write_xas_proc(
                 _logger.info("{} is not available".format(plot.signal))
             else:
                 link_dataset(dataset_to_link=signal_dataset, name=plot.signal)
-            plot_group.attrs["signal"] = plot.signal
             # handle axes
             for axe in plot.axes:
                 try:
@@ -487,7 +485,7 @@ def write_xas_proc(
                     _logger.info("{} is not available".format(axe))
                 else:
                     link_dataset(dataset_to_link=axe_dataset, name=axe)
-            plot_group.attrs["axes"] = plot.axes
+
             # handle auxiliary signals
             if plot.auxiliary_signals is not None:
                 for aux_sig in plot.auxiliary_signals:
@@ -499,17 +497,24 @@ def write_xas_proc(
                         link_dataset(dataset_to_link=aux_sig_dataset, name=aux_sig)
 
                 plot_group.attrs["auxiliary_signals"] = plot.auxiliary_signals
-            # handle title(s)
-            if plot.title is not None:
-                plot_group.attrs["title"] = plot.title
-            if plot.title_latex is not None:
-                plot_group.attrs["title_latex"] = plot.title_latex
 
-            # handle silx style
-            if plot.silx_style is not None:
-                import json
+        nexus_dict = {
+            "@NX_class": "NXdata",
+            "@interpretation": "spectrum",
+            "@signal": plot.signal,
+            "@axes": plot.axes,
+        }
+        # handle title(s)
+        if plot.title is not None:
+            nexus_dict["@title"] = plot.title
+        if plot.title_latex is not None:
+            nexus_dict["@title_latex"] = plot.title_latex
+
+        # handle silx style
+        if plot.silx_style is not None:
+            nexus_dict["@SILX_style"] = json.dumps(plot.silx_style)
 
-                plot_group.attrs["SILX_style"] = json.dumps(plot.silx_style)
+        dicttonx(nexus_dict, h5_file, mode="a", h5path=plot_path, update_mode="replace")
 
     # save plots
     for i_plot, plot in enumerate(plots):
@@ -519,10 +524,13 @@ def write_xas_proc(
     # default plot will always be the first one
     if len(plots) > 0:
         plots_path = "/".join((entry, process_name, "plots"))
-        with HDF5File(h5_file, "a") as h5f:
-            plots_group = h5f.require_group(plots_path)
-            plots_group.attrs["NX_class"] = "NXdata"
-            plots_group.attrs["default"] = "plot_0"
+        nexus_dict = {
+            "@NX_class": "NXdata",
+            "@default": "plot_0",
+        }
+        dicttonx(
+            nexus_dict, h5_file, mode="a", h5path=plots_path, update_mode="replace"
+        )
 
     if process.getConfiguration() is not None:
         h5_path = "/".join((nx_process_path, "configuration"))
@@ -563,58 +571,38 @@ def write_xas(
     :param str title: experiment title
     :param str definition: experiment definition
     """
-    with HDF5File(h5_file, "w") as h5f:
-        nx_entry = h5f.require_group("/".join((data_path, entry)))
-        nx_entry.attrs["NX_class"] = "NXentry"
-
-        # store energy
-        nx_monochromator = nx_entry.require_group("monochromator")
-        nx_monochromator.attrs["NX_class"] = "NXmonochromator"
-        if overwrite and "energy" in nx_monochromator:
-            del nx_monochromator["energy"]
-        nx_monochromator["energy"] = energy
-        nx_monochromator["energy"].attrs["interpretation"] = "spectrum"
-        nx_monochromator["energy"].attrs["NX_class"] = "NXdata"
-        nx_monochromator["energy"].attrs["unit"] = "eV"
-
-        # store absorbed beam
-        nx_absorbed_beam = nx_entry.require_group("absorbed_beam")
-        nx_absorbed_beam.attrs["NX_class"] = "NXdetector"
-        if overwrite and "data" in nx_absorbed_beam:
-            del nx_absorbed_beam["data"]
-        nx_absorbed_beam["data"] = mu
-        nx_absorbed_beam["data"].attrs["interpretation"] = "image"
-        nx_absorbed_beam["data"].attrs["NX_class"] = "NXdata"
-
-        if sample:
-            nx_sample = nx_entry.require_group("sample")
-            nx_sample.attrs["NX_class"] = "NXsample"
-            if overwrite and "name" in nx_sample:
-                del nx_sample["name"]
-            nx_sample["name"] = sample.name
-
-        nx_data = nx_entry.require_group("data")
-        nx_data.attrs["NX_class"] = "NXdata"
-        # create some link on data
-        if overwrite and "energy" in nx_data:
-            del nx_data["energy"]
-        nx_data["energy"] = h5py.SoftLink(nx_monochromator["energy"].name)
-        if overwrite and "absorbed_beam" in nx_data:
-            del nx_data["absorbed_beam"]
-        nx_data["absorbed_beam"] = h5py.SoftLink(nx_absorbed_beam["data"].name)
-
-        if start_time is not None:
-            if overwrite and "start_time" in nx_entry:
-                del nx_entry["start_time"]
-            nx_entry["start_time"] = start_time
-        if title is not None:
-            if overwrite and "title" in nx_entry:
-                del nx_entry["title"]
-            nx_entry["title"] = title
-        if definition is not None:
-            if overwrite and "definition" in nx_entry:
-                del nx_entry["definition"]
-            nx_entry["definition"] = definition
+    h5path = "/".join((data_path, entry))
+    nx_dict = {
+        "@NX_class": "NXentry",
+        "monochromator": {
+            "@NX_class": "NXmonochromator",
+            "energy": energy,
+            "energy@interpretation": "spctrum",
+            "energy@NX_class": "NXdata",
+            "energy@unit": "eV",
+        },
+        "absorbed_beam": {
+            "@NX_class": "NXdetector",
+            "data": mu,
+            "data@interpretation": "image",
+            "data@NX_class": "NXdata",
+        },
+        "data": {
+            "@NX_class": "NXdata",
+            ">energy": "../monochromator/energy",
+            ">absorbed_beam": "../absorbed_beam/data",
+        },
+        "start_time": start_time,
+        "title": title,
+        "definition": definition,
+    }
+    if overwrite:
+        mode = "w"
+        update_mode = "replace"
+    else:
+        mode = "a"
+        update_mode = "add"
+    dicttonx(nx_dict, h5_file, h5path=h5path, mode=mode, update_mode=update_mode)
 
 
 def write_spectrum_saving_pt(h5_file, entry, obj, overwrite=True):